Add motus prep_long

modules/nf-core/motus/preplong/environment.yml

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+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::motus=3.1.0

modules/nf-core/motus/preplong/main.nf

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+process MOTUS_PREPLONG {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/motus:3.1.0--pyhdfd78af_0':
+        'biocontainers/motus:3.1.0--pyhdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(reads)
+    path db
+
+    output:
+    tuple val(meta), path("*.gz"), emit: out
+    path "versions.yml"          , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def refdb = db ? "-db ${db}" : ""
+
+    """
+    motus \\
+        prep_long \\
+        $args \\
+        -i $reads \\
+        $refdb \\
+        -t $task.cpus \\
+        -o ${prefix}.gz \\
+        2> >(tee ${prefix}.log >&2)
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        motus: \$(motus --version 2>&1 | sed 's/.* \\([0-9]*\\.[0-9]*\\.[0-9]*\\) .*/\\1/')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    echo '' | gzip > ${prefix}.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        motus: \$(motus --version 2>&1 | sed 's/.* \\([0-9]*\\.[0-9]*\\.[0-9]*\\) .*/\\1/')
+    END_VERSIONS
+    """
+}

modules/nf-core/motus/preplong/meta.yml

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+name: "motus_preplong"
+description: Taxonomic meta-omics profiling using universal marker genes
+keywords:
+  - classify
+  - metagenomics
+  - fastq
+  - taxonomic profiling
+tools:
+  - "motus":
+      description: "Marker gene-based operational taxonomic unit (mOTU) profiling"
+      homepage: "https://motu-tool.org/"
+      documentation: "https://github.com/motu-tool/mOTUs/wiki"
+      tool_dev_url: "https://github.com/motu-tool/mOTUs"
+      doi: "10.1186/s40168-022-01410-z"
+      licence: ["GPL v3"]
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - reads:
+        type: file
+        description: Long read file to convert, can be fasta(.gz) or fastq(.gz)
+        pattern: "*.{gz}"
+  - - db:
+        type: directory
+        description: |
+          mOTUs database downloaded by `motus downloadDB`
+          pattern: "db_mOTU/"
+output:
+  - out:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "*.gz":
+          type: file
+          description: converted file (gzipped), ready to be used by motus profile
+          pattern: "*.gz"
+  - versions:
+      - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+
+authors:
+  - "@sofstam"
+maintainers:
+  - "@sofstam"

modules/nf-core/motus/preplong/tests/main.nf.test

@@ -0,0 +1,75 @@
+nextflow_process {
+
+    name "Test Process MOTUS_PREPLONG"
+    script "../main.nf"
+    process "MOTUS_PREPLONG"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "motus"
+    tag "motus/downloaddb"
+    tag "motus/preplong"
+
+    setup {
+        run("MOTUS_DOWNLOADDB") {
+            script "modules/nf-core/motus/downloaddb/main.nf"
+            process {
+                """
+                input[0] = Channel.of([
+                    file('https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py')
+                ])
+                """
+            }
+        }
+    }
+
+    test("sarscov2 - fasta") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test_2.fastq.gz', checkIfExists: true)
+                ]
+                input[1] =  MOTUS_DOWNLOADDB.out.db
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - fasta - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test_2.fastq.gz', checkIfExists: true)
+                ]
+                input[1] =  MOTUS_DOWNLOADDB.out.db
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+
+    }
+
+}

modules/nf-core/motus/preplong/tests/main.nf.test.snap

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+{
+    "sarscov2 - fasta - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,8fc614f9fe354b0811def13c772bc6fb"
+                ],
+                "out": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,8fc614f9fe354b0811def13c772bc6fb"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.1"
+        },
+        "timestamp": "2024-09-06T16:29:18.602046"
+    },
+    "sarscov2 - fasta": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.gz:md5,37be4a7321bcb2fdae60affb21a1737c"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,8fc614f9fe354b0811def13c772bc6fb"
+                ],
+                "out": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.gz:md5,37be4a7321bcb2fdae60affb21a1737c"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,8fc614f9fe354b0811def13c772bc6fb"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.1"
+        },
+        "timestamp": "2024-09-06T15:55:48.439664"
+    }
+}

modules/nf-core/motus/preplong/tests/tags.yml

@@ -0,0 +1,2 @@
+motus/preplong:
+  - "modules/nf-core/motus/preplong/**"